1. How do I make sure students meet standards-and meet enough of them to make the effort worthwhile-in open-ended activities and projects?

You will need to intergrate diffferent subjects to make this project worthwhile, using TIA, pacing guides and make sure that you are covering the standards across the curriclum. Even though your unit's focus is 'science' the other subjects will be covered. Use variety of assessment to check student's understanding and mastery.